Name: rs11530549
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs11530549

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:114636039 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: G>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.091416 (24197/264690, TOPMED)
A=0.089663 (12539/139846, GnomAD)
A=0.17011 (4807/28258, 14KJPN) (+ 10 more)
A=0.10055 (1862/18518, ALFA)
A=0.16697 (2798/16758, 8.3KJPN)
A=0.0887 (568/6404, 1000G_30x)
A=0.1136 (332/2922, KOREAN)
A=0.1168 (214/1832, Korea1K)
A=0.111 (111/998, GoNL)
A=0.128 (77/600, NorthernSweden)
A=0.171 (37/216, Qatari)
G=0.47 (41/88, SGDP_PRJ)
A=0.05 (2/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: NXPE2 : Intron Variant
NXPE4 : Intron Variant
Publications: 0 citations
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18518	G=0.89945	A=0.10055
European	Sub	14150	G=0.88558	A=0.11442
African	Sub	2898	G=0.9634	A=0.0366
African Others	Sub	114	G=0.991	A=0.009
African American	Sub	2784	G=0.9623	A=0.0377
Asian	Sub	112	G=0.920	A=0.080
East Asian	Sub	86	G=0.94	A=0.06
Other Asian	Sub	26	G=0.85	A=0.15
Latin American 1	Sub	146	G=0.870	A=0.130
Latin American 2	Sub	610	G=0.923	A=0.077
South Asian	Sub	98	G=0.90	A=0.10
Other	Sub	504	G=0.897	A=0.103

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	G=0.908584	A=0.091416
gnomAD - Genomes	Global	Study-wide	139846	G=0.910337	A=0.089663
gnomAD - Genomes	European	Sub	75732	G=0.88264	A=0.11736
gnomAD - Genomes	African	Sub	41916	G=0.96290	A=0.03710
gnomAD - Genomes	American	Sub	13610	G=0.90617	A=0.09383
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.8902	A=0.1098
gnomAD - Genomes	East Asian	Sub	3126	G=0.9264	A=0.0736
gnomAD - Genomes	Other	Sub	2138	G=0.8952	A=0.1048
14KJPN	JAPANESE	Study-wide	28258	G=0.82989	A=0.17011
Allele Frequency Aggregator	Total	Global	18518	G=0.89945	A=0.10055
Allele Frequency Aggregator	European	Sub	14150	G=0.88558	A=0.11442
Allele Frequency Aggregator	African	Sub	2898	G=0.9634	A=0.0366
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.923	A=0.077
Allele Frequency Aggregator	Other	Sub	504	G=0.897	A=0.103
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.870	A=0.130
Allele Frequency Aggregator	Asian	Sub	112	G=0.920	A=0.080
Allele Frequency Aggregator	South Asian	Sub	98	G=0.90	A=0.10
8.3KJPN	JAPANESE	Study-wide	16758	G=0.83303	A=0.16697
1000Genomes_30x	Global	Study-wide	6404	G=0.9113	A=0.0887
1000Genomes_30x	African	Sub	1786	G=0.9804	A=0.0196
1000Genomes_30x	Europe	Sub	1266	G=0.8649	A=0.1351
1000Genomes_30x	South Asian	Sub	1202	G=0.8644	A=0.1356
1000Genomes_30x	East Asian	Sub	1170	G=0.9085	A=0.0915
1000Genomes_30x	American	Sub	980	G=0.906	A=0.094
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.8864	A=0.1136
Korean Genome Project	KOREAN	Study-wide	1832	G=0.8832	A=0.1168
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.889	A=0.111
Northern Sweden	ACPOP	Study-wide	600	G=0.872	A=0.128
Qatari	Global	Study-wide	216	G=0.829	A=0.171
SGDP_PRJ	Global	Study-wide	88	G=0.47	A=0.53
The Danish reference pan genome	Danish	Study-wide	40	G=0.95	A=0.05

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 11	NC_000011.10:g.114636039G>A
GRCh37.p13 chr 11	NC_000011.9:g.114506761G>A

Gene: NXPE4, neurexophilin and PC-esterase domain family member 4 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NXPE4 transcript variant 1	NM_001077639.2:c.	N/A	Genic Upstream Transcript Variant
NXPE4 transcript variant 2	NM_017678.3:c.	N/A	Genic Upstream Transcript Variant
NXPE4 transcript variant X1	XM_047427147.1:c.-114+122… XM_047427147.1:c.-114+12202C>T	N/A	Intron Variant
NXPE4 transcript variant X2	XM_047427148.1:c.-114+122… XM_047427148.1:c.-114+12202C>T	N/A	Intron Variant
NXPE4 transcript variant X3	XM_047427149.1:c.-114+122… XM_047427149.1:c.-114+12202C>T	N/A	Intron Variant
NXPE4 transcript variant X4	XM_047427150.1:c.-114+122… XM_047427150.1:c.-114+12202C>T	N/A	Intron Variant
NXPE4 transcript variant X5	XM_047427151.1:c.-114+122… XM_047427151.1:c.-114+12202C>T	N/A	Intron Variant
NXPE4 transcript variant X10	XM_006718865.4:c.	N/A	Genic Upstream Transcript Variant
NXPE4 transcript variant X7	XM_011542881.3:c.	N/A	Genic Upstream Transcript Variant
NXPE4 transcript variant X8	XM_011542882.3:c.	N/A	Genic Upstream Transcript Variant
NXPE4 transcript variant X9	XM_011542883.3:c.	N/A	Genic Upstream Transcript Variant
NXPE4 transcript variant X6	XM_047427152.1:c.	N/A	Genic Upstream Transcript Variant

Gene: NXPE2, neurexophilin and PC-esterase domain family member 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NXPE2 transcript	NM_182495.6:c.	N/A	Genic Upstream Transcript Variant
NXPE2 transcript variant X2	XM_017017207.2:c.-46-4361… XM_017017207.2:c.-46-43618G>A	N/A	Intron Variant
NXPE2 transcript variant X3	XM_017017209.2:c.-46-4361… XM_017017209.2:c.-46-43618G>A	N/A	Intron Variant
NXPE2 transcript variant X4	XM_011542604.3:c.	N/A	Genic Upstream Transcript Variant
NXPE2 transcript variant X1	XM_017017206.2:c.	N/A	Genic Upstream Transcript Variant
NXPE2 transcript variant X5	XM_017017211.2:c.	N/A	Genic Upstream Transcript Variant
NXPE2 transcript variant X6	XM_017017212.2:c.	N/A	Genic Upstream Transcript Variant
NXPE2 transcript variant X7	XR_001747769.2:n.	N/A	Genic Upstream Transcript Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	G=	A
GRCh38.p14 chr 11	NC_000011.10:g.114636039=	NC_000011.10:g.114636039G>A
GRCh37.p13 chr 11	NC_000011.9:g.114506761=	NC_000011.9:g.114506761G>A
NXPE2 transcript variant X2	XM_017017207.2:c.-46-43618=	XM_017017207.2:c.-46-43618G>A
NXPE2 transcript variant X3	XM_017017209.2:c.-46-43618=	XM_017017209.2:c.-46-43618G>A
NXPE4 transcript variant X1	XM_047427147.1:c.-114+12202=	XM_047427147.1:c.-114+12202C>T
NXPE4 transcript variant X2	XM_047427148.1:c.-114+12202=	XM_047427148.1:c.-114+12202C>T
NXPE4 transcript variant X3	XM_047427149.1:c.-114+12202=	XM_047427149.1:c.-114+12202C>T
NXPE4 transcript variant X4	XM_047427150.1:c.-114+12202=	XM_047427150.1:c.-114+12202C>T
NXPE4 transcript variant X5	XM_047427151.1:c.-114+12202=	XM_047427151.1:c.-114+12202C>T

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

29 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss16120928	Feb 28, 2004 (120)
2	SC_SNP	ss18477287	Feb 28, 2004 (126)
3	GMI	ss281179838	May 04, 2012 (142)
4	GMI	ss286462091	Apr 25, 2013 (142)
5	1000GENOMES	ss337001036	May 09, 2011 (142)
6	SSMP	ss658364319	Apr 25, 2013 (142)
7	EVA-GONL	ss988987186	Aug 21, 2014 (142)
8	EVA_GENOME_DK	ss1575967042	Apr 01, 2015 (144)
9	WEILL_CORNELL_DGM	ss1932348979	Feb 12, 2016 (147)
10	JJLAB	ss2026918139	Sep 14, 2016 (149)
11	GRF	ss2699541638	Nov 08, 2017 (151)
12	GNOMAD	ss2904722920	Nov 08, 2017 (151)
13	SWEGEN	ss3008817845	Nov 08, 2017 (151)
14	CSHL	ss3349806080	Nov 08, 2017 (151)
15	ACPOP	ss3738560002	Jul 13, 2019 (153)
16	EVA	ss3749841088	Jul 13, 2019 (153)
17	SGDP_PRJ	ss3877185905	Apr 26, 2020 (154)
18	KRGDB	ss3925645772	Apr 26, 2020 (154)
19	KOGIC	ss3970794331	Apr 26, 2020 (154)
20	TOPMED	ss4900797584	Apr 26, 2021 (155)
21	TOMMO_GENOMICS	ss5203993957	Apr 26, 2021 (155)
22	1000G_HIGH_COVERAGE	ss5288983657	Oct 16, 2022 (156)
23	EVA	ss5402394728	Oct 16, 2022 (156)
24	1000G_HIGH_COVERAGE	ss5585510335	Oct 16, 2022 (156)
25	SANFORD_IMAGENETICS	ss5652118757	Oct 16, 2022 (156)
26	TOMMO_GENOMICS	ss5752472101	Oct 16, 2022 (156)
27	YY_MCH	ss5812796174	Oct 16, 2022 (156)
28	EVA	ss5837261447	Oct 16, 2022 (156)
29	EVA	ss5943450397	Oct 16, 2022 (156)
30	1000Genomes_30x	NC_000011.10 - 114636039	Oct 16, 2022 (156)
31	The Danish reference pan genome	NC_000011.9 - 114506761	Apr 26, 2020 (154)
32	gnomAD - Genomes	NC_000011.10 - 114636039	Apr 26, 2021 (155)
33	Genome of the Netherlands Release 5	NC_000011.9 - 114506761	Apr 26, 2020 (154)
34	KOREAN population from KRGDB	NC_000011.9 - 114506761	Apr 26, 2020 (154)
35	Korean Genome Project	NC_000011.10 - 114636039	Apr 26, 2020 (154)
36	Northern Sweden	NC_000011.9 - 114506761	Jul 13, 2019 (153)
37	Qatari	NC_000011.9 - 114506761	Apr 26, 2020 (154)
38	SGDP_PRJ	NC_000011.9 - 114506761	Apr 26, 2020 (154)
39	8.3KJPN	NC_000011.9 - 114506761	Apr 26, 2021 (155)
40	14KJPN	NC_000011.10 - 114636039	Oct 16, 2022 (156)
41	TopMed	NC_000011.10 - 114636039	Apr 26, 2021 (155)
42	ALFA	NC_000011.10 - 114636039	Apr 26, 2021 (155)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID	History Updated (Build)
rs12224241	Oct 14, 2006 (127)
rs140672354	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss281179838, ss286462091	NC_000011.8:114011970:G:A	NC_000011.10:114636038:G:A	(self)
2744962, 13783598, 32823166, 11844867, 14390909, 29202885, 61963264, ss337001036, ss658364319, ss988987186, ss1575967042, ss1932348979, ss2026918139, ss2699541638, ss2904722920, ss3008817845, ss3349806080, ss3738560002, ss3749841088, ss3877185905, ss3925645772, ss5203993957, ss5402394728, ss5652118757, ss5837261447, ss5943450397	NC_000011.9:114506760:G:A	NC_000011.10:114636038:G:A	(self)
73036270, 392642824, 27172332, 86309205, 116343240, 7497393064, ss3970794331, ss4900797584, ss5288983657, ss5585510335, ss5752472101, ss5812796174	NC_000011.10:114636038:G:A	NC_000011.10:114636038:G:A	(self)
ss16120928, ss18477287	NT_033899.6:18050547:G:A	NC_000011.10:114636038:G:A	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs11530549

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
Top▲ Help
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs11530549